Beauchamp:Lab Notebook

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Revision as of 07:28, 27 September 2011 by Michael S Beauchamp (talk | contribs) (MRI: Cortical Surface Models)
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Brain picture
Beauchamp Lab

General Important Notes

  1. How To Install Software and set up new computers
  2. How To order things for the lab
  3. Information for Subjects and Experimenters, such as Human Subjects Training

MRI: Cortical Surface Models

Overview: There is a simple three step process for creating surface models. The steps assume that you are in the afni subdirectory of the subject for which a surface is to be created.

 cd /Volumes/data1/UT/IZ/afni

Step 1: Prepare the FreeSurfer directory tree

 /Volumes/data1/UT/scripts/@prep_dir IZanatavg+orig.BRIK  

Step 2: Reconstruct the surface. Note that no argument is required, but if you are using the up arrow to recall the last command and edit it, there is no need to remove the argument. /Volumes/data1/scripts/@recon IZanatavg+orig.BRIK Step 3: Finish the surface /Volumes/data1/scripts/@finish IZanatavg+orig.BRIK For more details, see the following web pages:

  1. Preparation for Creating Cortical Surface Models
  2. Creating Cortical Surface Models
  3. Final touches and using Cortical Surface Models
  4. What If a Cortical Surface Model Exists Already
  5. What If Cortical Surface Model Looks Bad
  6. Creating Standardized Surface Models
  7. FreeSurfer Standard Surface Models
  8. Finding Distances on the Surface
  9. Finding Closest node on the Surface
  10. SUMA
  11. Free Surfer
  12. Caret

MRI: fMRI Experimental Design and Analysis

  1. Creating Random Stimulus Orderings For Rapid Event-Related Designs
  2. Overview of fMRI Analysis
  3. Motion and Distortion Correction
  4. Creating AFNI BRIKs from MR Data
  5. Creating Volume Average Datasets with AFNI
  6. MVPA Notes
  7. RealTimefMRI
  8. Group Analysis with Unequal Group Sizes using GroupAna.m
  9. HiResolution fMRI
  10. ROI Analysis

MRI: DTI Analysis

  1. Processing Diffusion Tensor Imaging Data
  2. Automatic VOI Initialization for Interactive Tractography
  3. Deterministic Tractography Constrained by Image Masks


  1. Overview of an MRI/fMRI guided TMS Experiment
  2. Notes on TMS


  1. Eswen Fava's NIRS Manual


  1. Electrode Localization and Naming
  2. Electrophysiology Protocols
  3. Analyzing ECoG data (by Adam Burch)
  4. Making Resting State Correlation Maps


  1. New Auditory Tactile Experiment
  2. d' (d-prime) Analysis
  3. Race Model Analysis
  4. Stimuli for 100 Hue Experiment

Misc. Experiment Notes

  1. McGurk Stimuli
  2. Autism Data
  3. Scanner Stimulus and Eye Tracker Setup
  4. Retinotopic Mapping
  5. AFNI Atlas Values
  6. Tactile Experiment Notes
  7. Notes on analyzing MRI data (old)